NUT Midline Carcinoma
NUT midline carcinoma, or “NMC,” is a rare form of cancer characterized by a chromosomal rearrangement in which a portion of the NUT (nuclear protein in testis) gene on chromosome 15 is fused to a BRD (bromodomain protein) gene or other, as yet unidentified, gene (French, et al., Cancer Res. 63(2):304-307 (2003); French, et al., J. Clin. Oncol. 22(20):4135-4139 (2004); French, et al., Oncogene 27(15):2237-2242 (Apr. 3, 2007)). NUT fusion genes encode oncoproteins that maintain cells in an undifferentiated state and promote their rapid and uncontrolled growth. The frequent involvement of midline structures in the head, neck, mediastinal, and other midline structures, suggest that NMCs arise from primitive neural crest-derived cells. NMCs are very aggressive clinically, respond poorly to conventional chemotherapy, and are almost uniformly fatal.
BRD4 was originally named MCAP (Mitotic Chromosome-Associated Protein) because it remains bound to chromatin via its two bromodomains during mitosis. It is thought to bind in the region of actively transcribed genes before mitosis, thus providing a kind of cellular memory that ensures re-initiation of transcription from these sites after mitosis is completed. Two recent studies provide evidence that this may indeed be the case (Yang, et al., Mol. Cell Biol. 28(3):967-76 (2008); Mochizuki, et al., J. Biol. Chem. 283(14):9040-9048 (2008)). The function of BRD3 is less well characterized but, like all proteins in the BRD family, it contains two acetyl-histone-binding bromodomains and an extra terminal domain (Wu, et al., J. Biol. Chem. 282(18):13141-13145 (2007); Thorpe, et al., Gene 200(1-2):177-183 (1997)). BRD3 is highly homologous to BRD4 and so its involvement in NMC is not unexpected. About two thirds of NMCs result from fusion of NUT to BRD4, and the remaining result from fusion of NUT to BRD3 or other, as yet uncharacterized, gene (French et al., Oncogene 27 (15):2237-2242 (Apr. 3, 2007)).
In contrast to BRD proteins, NUT lacks known functional domains, is poorly conserved, and is apparently restricted to mammals. Although NUT normally shuttles between the nucleus and cytoplasm, it remains bound to chromatin when fused to BRD4 or BRD3 (French, et al., Oncogene 27(15):2237-2242 (Apr. 3, 2007)). This suggests that the BRD moiety of the fusion protein serves to tether NUT to chromatin, thus modifying the function of either or both proteins in a way that affects transcription. One important consequence of BRD-NUT expression has been discovered using siRNA to silence the expression of BRD3- or BRD4-NUT in NMC cell lines. It was found that withdrawal of the NUT fusion proteins resulted in irreversible squamous differentiation and arrested growth (French, et al., Oncogene 27(15):2237-2242 (Apr. 3, 2007)). These findings suggest that BRD-NUT proteins block differentiation.
Histone Deacetylase Inhibitors
During the last few years, it has become increasingly clear that the acetylation of histones plays a central role in the structure of chromatin and gene regulation. Acetylation reduces the positive charge of histones, thereby relaxing the structure of the nucleosome and facilitating the interaction of transcription factors with DNA. Removal of the acetyl group restores the positive charge, thereby causing the nucleosome to contract and become less accessible to transcription factors (Wade et al., Trends Biochem. Sci. 22:128 132 (1997); and Wolffe, Science 272:371-372 (1996)).
Histone deacetylases (HDACs) catalyze the removal of acetyl groups from histones and appear to play a particularly important role in regulating gene expression. HDACs are segregated into four functionally related classes based on sequence homology to characterized yeast proteins Inhibition of class I HDACs has been actively pursued as an anticancer strategy due to epigenetic changes that affect gene expression in cancer cells. At least one HDAC inhibitor, vorinostat, has been approved by the FDA for use in certain cancers. Activity has been documented in hematologic malignancies, in particular, cutaneous T-cell lymphoma (Minucci, et al., Nature Reviews 6(1):38-51 (2006); Duvic, et al., Blood 109(1):31-39 (2007)). Dose-limiting toxicities for this class of drug include fatigue, nausea, lethargy and myelosuppression, in particular thrombocytopenia.